Team:York/Notebook

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Keeping Track of Progress

Notebook

Week 1 (19 June - 25 June)

  • Biology Division

    First week detailed experementation plan and lab supplies ordering.

  • Microscopy Division

    Had a first meeting of your division. Discussed timeline and the components we have available. For now, we will order only camera. Figured out that Biology Labs do not have any lasers and optical benches.



Week 2 (26 June - 2 July)

  • Biology Division

    Biology Lab Safety talk for all team members. Prepared LB media for E.coli and pored it into plates. Freezig E.coli cells for an emergency. Checking plates for algae and liquid culture for transformation. Prepared for plasmid extraction via electrophoresis.

  • Microscopy Division

    We were given access to Physics Labs. It will be our home for the next weeks. We watched laser safety video and started taking pictures with freshly arrived Raspberry Pi V2 Camera. Made prototype of the DIHM. How easy was that?!



Week 3 (3 July - 9 July)

  • Biology Division

    Digested pLM005. Prepared TAP media plates for algae. Performed colony PCR for ACA3.

  • Microscopy Division

    Flower shape leaves pictures were obtained by shining laser on camera. Problem might be in IR filter on the lens of the camera. We ordered Raspberry Pi V2 NoIR camera which does not have IR filter. While waiting for a new camera, we were trying to make Rapsberry Pi to sent pictures automatically to desktop computer.





Week 4 (10 July - 16 July)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Received NoIR camera. Leaves shape pattern solved. We were trying to observe diffraction from single slit experiment with a laser. Intensity of a laser was lowered with polarisation filter to avoid overexposure of camera. We used converging lens available in the lab to focus diffraction pattern on CMOS. Unfortunately, it was hard to setup to capture clear image. We are thinking to acquire lens with small focal distance to make setup as compact as possible.





Week 5 (17 July - 23 July)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Removed lens from camera which was done easily. Now, light is shinning directly on CMOS. Still we have problems with alignment of laser, slits and camera. Moreover, single slit was too bright for naked CMOS. Now, we are using double slit experiment to observe interference in best tradition of Thomas Young.



Week 6 (24 July - 30 July)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    After imaging double slit interference pattern we are moving to object imaging comperable with microorganisms size - microbeads. In parallel, we are translating software code for image reconstruction from LabVIEW to MATLAB. We received laser from TU Darmstadt team which is iterested in building DIHM, too.







Week 7 (31 July - 6 August)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    We were able to see single microbeads with our setup. Now, we have to be technical and measure precisely distances need for fully working DIHM. Also, we met with Dr Wilson to discuss our progress so far.





Week 8 (7 August - 13 August)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Looks like we will have to make image analysis in Python for a beginning. We still see the noise on captured images.



Week 9 (14 August - 20 August)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Last week we ordered a new laser and quality of the image changed drastically. Laser that we were using in the lab was inappropriate for Digital Holography as we have figured that out.



Week 10 (21 August - 27 August)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Image recostruction software is almost ready. We are thinking about the design of DIHM and seeking for inspiration around the campus. Teflon mold was made for us this week which we will use to cast PDMS.



Week 11 (28 August - 3 September)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    We find difficult to attach PDMS chamber to a glass slide. We met with plasma researcher in your university to discuss plasma bonding options. Whereas, UI for image capturing and analysis is rapidly developed.







Week 12 (4 September - 10 September)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    We abandoned idea of using PDMS as a material for imaging chamber. Aluminium case for our microscope is ready. We hope to get all parts by next week.



Week 13 (11 September - 17 September)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Solution for imaging chamber was found by using acryl sheets and laser cutting. Desktop does not want to communicate with Raspberry Pi, but we will reconcile them.



Week 14 (18 September - 24 September)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    We have imaged Chlamydomonas reinhardtii and E.coli separately and together. We figured out that millichamber we have manufactured are too thick for your laser. Instead, we are using glass slide and coverslip. UI is completed.



Week 15 (25 September - 1 October)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    We compared results from last week imaging and automated cell counter. It looks like our setup is working and we are able to calculate concetration of the microorganisms. We will do imaging of yeast and other bacteria and algae.



Week 16 (2 October - 8 October)

  • Biology Division

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. In eu vulputate dolor. Ut euismod nulla a efficitur placerat. Quisque eget nisl in eros mollis sagittis. Aliquam pretium feugiat nulla, quis aliquam lorem suscipit bibendum. Interdum et malesuada fames ac ante ipsum primis in faucibus.

  • Microscopy Division

    Not much progress was done on laptop-microscope connection.



  • ABOUT US
  • We are an overgraduate team representing the University of York.
  • Our Quicker Way to Analyse Co-Cultures (QWACC) is our entry into the Hardware track for iGEM 2017.
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